Structural basis of circularly permuted group II intron self-splicing

Pyle, A. M. Group II intron self-splicing. Annu. Rev. Biophys. 45, 183–205 (2016).

Article  CAS  PubMed  Google Scholar 

Lambowitz, A. M. & Zimmerly, S. Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb. Perspect. Biol. 3, a003616 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Pyle, A. & Lambowitz, A. in The RNA World 3rd edn (eds Gesteland, R. F. et al.) 469–505 (Cold Spring Harbor Laboratory, 2006).

Zimmerly, S. & Semper, C. Evolution of group II introns. Mob. DNA 6, 7 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Lambowitz, A. M. & Belfort, M. in Mobile DNA III (eds Chandler, M. et al.) 1209–1236 (ASM, 2015).

Galej, W. P., Toor, N., Newman, A. J. & Nagai, K. Molecular mechanism and evolution of nuclear pre-mRNA and group II intron splicing: insights from cryo-electron microscopy structures. Chem. Rev. 118, 4156–4176 (2018).

Article  CAS  PubMed  Google Scholar 

Wilkinson, M. E., Charenton, C. & Nagai, K. RNA splicing by the spliceosome. Annu. Rev. Biochem. 89, 359–388 (2020).

Article  CAS  PubMed  Google Scholar 

Xu, L., Liu, T., Chung, K. & Pyle, A. M. Structural insights into intron catalysis and dynamics during splicing. Nature 624, 682–688 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haack, D. B. et al. Cryo-EM structures of a group II intron reverse splicing into DNA. Cell 178, 612–623.e12 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pan, T. & Uhlenbeck, O. C. Circularly permuted DNA, RNA and proteins—a review. Gene 125, 111–114 (1993).

Article  CAS  PubMed  Google Scholar 

Grishin, N. V. Fold change in evolution of protein structures. J. Struct. Biol. 134, 167–185 (2001).

Article  CAS  PubMed  Google Scholar 

Bliven, S. & Prlić, A. Circular permutation in proteins. PLoS Comput. Biol. 8, e1002445 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ford, E. & Ares, M. Synthesis of circular RNA in bacteria and yeast using RNA cyclase ribozymes derived from a group I intron of phage T4. Proc. Natl Acad. Sci. USA 91, 3117–3121 (1994).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jarrell, K. A. Inverse splicing of a group II intron. Proc. Natl Acad. Sci. USA 90, 8624–8627 (1993).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, C.-X. & Chen, L.-L. Circular RNAs: characterization, cellular roles, and applications. Cell 185, 2016–2034 (2022).

Article  CAS  PubMed  Google Scholar 

Qu, L. et al. Circular RNA vaccines against SARS-CoV-2 and emerging variants. Cell 185, 1728–1744.e16 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roth, A., Weinberg, Z., Vanderschuren, K., Murdock, M. H. & Breaker, R. R. Natural circularly permuted group II introns in bacteria produce RNA circles. iScience 24, 103431 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, C. et al. A flexible, efficient, and scalable platform to produce circular RNAs as new therapeutics. Preprint at bioRxiv https://doi.org/10.1101/2022.05.31.494115 (2022).

Ma, H., Jia, X., Zhang, K. & Su, Z. Cryo-EM advances in RNA structure determination. Signal Transduct. Target. Ther. 7, 58 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo, B. et al. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nat. Catal. 6, 298–309 (2023).

Article  CAS  Google Scholar 

Li, S., Palo, M. Z., Zhang, X., Pintilie, G. & Zhang, K. Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Nat. Commun. 14, 1294 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, X., Li, S., Pintilie, G., Palo, M. Z. & Zhang, K. Snapshots of the first-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Nucleic Acids Res. 51, 1317–1325 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Steitz, T. A. & Steitz, J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498–6502 (1993).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Heilman-Miller, S. L. & Woodson, S. A. Effect of transcription on folding of the Tetrahymena ribozyme. RNA 9, 722–733 (2003).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Toor, N., Keating, K. S., Taylor, S. D. & Pyle, A. M. Crystal structure of a self-spliced group II intron. Science 320, 77–82 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haack, D. B., Rudolfs, B., Zhang, C., Lyumkis, D. & Toor, N. Structural basis of branching during RNA splicing. Nat. Struct. Mol. Biol. 31, 179–189 (2024).

Article  CAS  PubMed  Google Scholar 

Erat, M. C. & Sigel, R. K. O. Divalent metal ions tune the self-splicing reaction of the yeast mitochondrial group II intron Sc.ai5γ. J. Biol. Inorg. Chem. 13, 1025–1036 (2008).

Article  CAS  PubMed  Google Scholar 

Marcia, M. & Pyle, A. M. Visualizing group II intron catalysis through the stages of splicing. Cell 151, 497–507 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nguyen, T. H. D. et al. CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. Curr. Opin. Struct. Biol. 36, 48–57 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boudvillain, M., de Lencastre, A. & Pyle, A. M. A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron. Nature 406, 315–318 (2000).

Article  CAS  PubMed  Google Scholar 

Costa, M. & Michel, F. Frequent use of the same tertiary motif by self‐folding RNAs. EMBO J. 14, 1276–1285 (1995).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boudvillain, M. & Marie Pyle, A. Defining functional groups, core structural features and inter‐domain tertiary contacts essential for group II intron self‐splicing: a NAIM analysis. EMBO J. 17, 7091–7104 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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